Application of Information Technology: An Integrated Software Suite for Surface-based Analyses of Cerebral Cortex

The authors describe and illustrate an integrated trio of software programs for carrying out surface-based analyses of cerebral cortex. The first component of this trio, SureFit (Surface Reconstruction by Filtering and Intensity Transformations), is used primarily for cortical segmentation, volume visualization, surface generation, and the mapping of functional neuroimaging data onto surfaces. The second component, Caret (Computerized Anatomical Reconstruction and Editing Tool Kit), provides a wide range of surface visualization and analysis options as well as capabilities for surface flattening, surface-based deformation, and other surface manipulations. The third component, SuMS (Surface Management System), is a database and associated user interface for surface-related data. It provides for efficient insertion, searching, and extraction of surface and volume data from the database.

[1]  Guillermo Sapiro,et al.  Creating connected representations of cortical gray matter for functional MRI visualization , 1997, IEEE Transactions on Medical Imaging.

[2]  William Schroeder,et al.  The Visualization Toolkit: An Object-Oriented Approach to 3-D Graphics , 1997 .

[3]  D. V. van Essen,et al.  Computerized Mappings of the Cerebral Cortex: A Multiresolution Flattening Method and a Surface-Based Coordinate System , 1996, Journal of Cognitive Neuroscience.

[4]  Rangasami L. Kashyap,et al.  Building Skeleton Models via 3-D Medial Surface/Axis Thinning Algorithms , 1994, CVGIP Graph. Model. Image Process..

[5]  D C Van Essen,et al.  'The surface management system' (SuMS) database: a surface-based database to aid cortical surface reconstruction, visualization and analysis. , 2001, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

[6]  E. Pennisi.  Finally, the Book of Life and Instructions for Navigating It , 2000, Science.

[7]  D. V. van Essen,et al.  Structural and Functional Analyses of Human Cerebral Cortex Using a Surface-Based Atlas , 1997, The Journal of Neuroscience.

[8]  J. Maunsell,et al.  Two‐dimensional maps of the cerebral cortex , 1980, The Journal of comparative neurology.

[9]  William E. Lorensen,et al.  Marching cubes: A high resolution 3D surface construction algorithm , 1987, SIGGRAPH.

[10]  D. V. Essen,et al.  Analysis and comparison of areal partitioning schemes using two-dimensional fluid deformations , 1996, NeuroImage.

[11]  D. J. Felleman,et al.  Distributed hierarchical processing in the primate cerebral cortex. , 1991, Cerebral cortex.

[12]  D. V. van Essen,et al.  Mapping of architectonic subdivisions in the macaque monkey, with emphasis on parieto‐occipital cortex , 2000, The Journal of comparative neurology.

[13]  A. Dale,et al.  High‐resolution intersubject averaging and a coordinate system for the cortical surface , 1999, Human brain mapping.

[14]  D. Whitteridge,et al.  The representation of the visual field on the cerebral cortex in monkeys , 1961, The Journal of physiology.

[15]  Eric L. Schwartz,et al.  A Numerical Solution to the Generalized Mapmaker's Problem: Flattening Nonconvex Polyhedral Surfaces , 1989, IEEE Trans. Pattern Anal. Mach. Intell..

[16]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[17]  B. Geiger.  Three-dimensional modeling of human organs and its application to diagnosis and surgical planning , 1993 .

[18]  W. Singer,et al.  Functional imaging of mirror and inverse reading reveals separate coactivated networks for oculomotion and spatial transformations , 1998, Neuroreport.

[19]  H A Drury,et al.  Computational methods for reconstructing and unfolding the cerebral cortex. , 1995, Cerebral cortex.

[20]  Gerald E. Farin,et al.  The geometry toolbox - for graphics and modeling , 1998 .

[21]  Abraham Z. Snyder,et al.  Surface-Based Analyses of the Human Cerebral Cortex , 1999 .

[22]  C. Gross,et al.  Visual topography of striate projection zone (MT) in posterior superior temporal sulcus of the macaque. , 1981, Journal of neurophysiology.

[23]  E. Marshall.  Rival Genome Sequencers Celebrate a Milestone Together , 2000, Science.

[24]  P. Goldman-Rakic,et al.  Preface: Cerebral Cortex Has Come of Age , 1991 .

[25]  Anders M. Dale,et al.  Cortical Surface-Based Analysis I. Segmentation and Surface Reconstruction , 1999, NeuroImage.

[26]  D. C. Essen,et al.  The topographic organization of rhesus monkey prestriate cortex. , 1978, The Journal of physiology.

[27]  R. Goebel.  A fast automated method for flattening cortical surfaces , 2000, NeuroImage.

[28]  Michael I. Miller,et al.  Landmark matching on brain surfaces via large deformation diffeomorphisms on the sphere , 1999, Medical Imaging.

[29]  Muge M. Bakircioglu,et al.  Mapping visual cortex in monkeys and humans using surface-based atlases , 2001, Vision Research.

[30]  D. V. van Essen,et al.  Functional and structural mapping of human cerebral cortex: solutions are in the surfaces. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[31]  B. Wandell,et al.  Visualization and Measurement of the Cortical Surface , 2000, Journal of Cognitive Neuroscience.

[32]  M. Corbetta,et al.  A Common Network of Functional Areas for Attention and Eye Movements , 1998, Neuron.

[33]  A. Dale,et al.  Cortical Surface-Based Analysis II: Inflation, Flattening, and a Surface-Based Coordinate System , 1999, NeuroImage.